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\name{toGRangesList-methods}
\docType{methods}
\alias{toGRangesList}
\alias{toGRangesList-methods}
\alias{toGRangesList,SitePairSetList,Axt-method}
\title{toGRangesList function}
\description{
Get the genomic coordinates from SitePairSetList.
}
\section{Methods}{
\describe{
\item{\code{signature(x = "SitePairSetList", axt = "Axt")}}{
Convert the relative coordinates to absolute coordinates.
}
}}
\value{
A list of two \code{GRanges} objects are returned,
one for the target sequences
and another for query sequences.
In the \code{GRanges}, strand is taken from the \code{Axt} object.
In the meta-data columns, PWM matrix ID, the strand of matrix and
match score are also returned.
}
\author{
Ge Tan
}
\examples{
data(MA0003.2)
pwm <- toPWM(MA0003.2)
library(CNEr)
axtFilesHg19DanRer7 <- file.path(system.file("extdata", package="TFBSTools"),
"hg19.danRer7.net.axt")
axtHg19DanRer7 <- readAxt(axtFilesHg19DanRer7)
sitePairSet <- searchAln(pwm, axtHg19DanRer7, min.score="80\%",
windowSize=51L, cutoff=0.7, strand="*",
type="any", conservation=NULL, mc.cores=1)
toGRangesList(sitePairSet, axtHg19DanRer7)
}
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